Stitch Interactive Report Run: Umab_mc
Generated at 2024-09-19 15:50:00
High decoy scores
The highest scoring decoy template scores at least 50% of the actual templates in template matching. Look into the Decoy segment for more details.
Maybe the origin of this issue is one of the following:
A sample with very high background noise, in that case the result should be thoroughly checked by hand.
Incorrect segments chosen, the chosen segments should match the expected segments and species of the dataset.
Homo sapiens Heavy Chain
EVQLVQSGAEVKKPGESLKISGHGSGYSFTTYWIGWVRQMPNKLDWLGIMSPVDSDLRYSPSFQGQVTMSVDKSITTAYLQWNSLKASDTAMYYHAQRPQFPFDFWGQGTLVTVSSSSTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSTVVTVPSSSLTTQTYIYDVQQKYSNTTVCKKYEPATGTPTHTCPPCPAPELLGLPSLFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTPVRQEQAALTRRVVSVLTVLHQDWLNGKEYKYKVSNKALPAPIEKVISKAKGQPREPQVYTLPPSRDELTKNQVSLTDLVKGFYPSDIAVEWEFDGSQPENNQKTTPPVLDSDGSFFLYSKLTVDKSRSCQGGVSSCSVMHEALHNHYTQASLPLSPGG
Depth of Coverage
Best scoring segments
Homo sapiens Light Chain
DIQMTQSPSSLSASVGDRVTITCRASQGISSWLAWYQQKPEKAPKSLIYAASSLQSGVPSRFSGSGSGPDLTLTITLLLPEDFATYYQCQYNLYPYTFGQGTKLEIKTRVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPRGLAKVQWKVDGQLQSGNSQESVTEQDSKDSTLTLNNDLTLLKADYEKHKVYACEVTHQGLSSPVTKSFGRNEC
Depth of Coverage
Best scoring segments
1133 (10.89% of all input reads) reads where matched to this segment of these 209 (18.45% of all matched reads) were matched uniquely.
605 (5.81% of all input reads) reads where matched to this segment of these 39 (6.45% of all matched reads) were matched uniquely.
| Identifier | Length | Score | Matches | Unique Score | Unique Matches |
|---|---|---|---|---|---|
| IGHG3 | 377 | 2.889E+04 | 346 | 0 | 0 |
| IGHG2 | 326 | 2.424E+04 | 290 | 62 | 1 |
| IGHG4 | 327 | 2.355E+04 | 282 | 0 | 0 |
| IGHV5-10-1 | 118 | 1.158E+04 | 127 | 426 | 6 |
| IGHV1-69 | 118 | 8863 | 93 | 169 | 2 |
| IGHV1-2 | 118 | 8494 | 91 | 105 | 2 |
| IGHV1-46 | 118 | 8407 | 89 | 0 | 0 |
| IGHV1-3 | 118 | 8407 | 89 | 0 | 0 |
| IGHV1-18 | 118 | 8296 | 88 | 0 | 0 |
| IGHV1-8 | 118 | 8260 | 88 | 45 | 1 |
| IGHV1-24 | 118 | 8206 | 87 | 0 | 0 |
| IGHV1-69-2 | 118 | 6175 | 65 | 0 | 0 |
| IGHV7-4-1 | 118 | 1178 | 15 | 0 | 0 |
| IGHV3-21 | 118 | 1111 | 17 | 0 | 0 |
| IGHV3-15 | 120 | 1007 | 15 | 0 | 0 |
| IGHV3-73 | 120 | 906 | 16 | 390 | 8 |
| IGHV3-11 | 118 | 822 | 13 | 81 | 1 |
| IGHV2-70 | 120 | 571 | 9 | 131 | 2 |
| IGHV3-74 | 118 | 438 | 7 | 0 | 0 |
| IGHV3-NL1 | 118 | 426 | 7 | 0 | 0 |
| IGHA1 | 323 | 403 | 6 | 125 | 2 |
| IGHV3-72 | 120 | 393 | 7 | 0 | 0 |
| IGHV3-64 | 118 | 386 | 7 | 0 | 0 |
| IGHV4-34 | 117 | 376 | 5 | 151 | 2 |
| IGHV3-13 | 117 | 341 | 6 | 0 | 0 |
| IGHV3-48 | 118 | 341 | 6 | 0 | 0 |
| IGHV3-7 | 118 | 341 | 6 | 0 | 0 |
| IGHV3-66 | 117 | 341 | 6 | 0 | 0 |
| IGHV3-23 | 118 | 341 | 6 | 0 | 0 |
| IGHV1-45 | 118 | 337 | 4 | 0 | 0 |
| IGHV3-20 | 118 | 329 | 6 | 0 | 0 |
| IGHV4-31 | 119 | 308 | 5 | 0 | 0 |
| IGHV3-30-5 | 118 | 296 | 5 | 0 | 0 |
| IGHV3-33 | 118 | 283 | 5 | 61 | 1 |
| IGHM | 453 | 271 | 5 | 210 | 4 |
| IGHV3-53 | 117 | 267 | 5 | 0 | 0 |
| IGHV6-1 | 121 | 264 | 4 | 174 | 3 |
| IGHA2 | 310 | 220 | 3 | 0 | 0 |
| IGHV3-30 | 118 | 211 | 4 | 0 | 0 |
| IGHE | 428 | 207 | 4 | 49 | 1 |
| IGHV4-30-4 | 119 | 206 | 3 | 0 | 0 |
| IGHV4-59 | 117 | 206 | 3 | 0 | 0 |
| IGHD | 385 | 196 | 4 | 106 | 2 |
| IGHV3-43 | 119 | 189 | 4 | 0 | 0 |
| IGHV1-58 | 118 | 148 | 3 | 0 | 0 |
| IGHV3-9 | 119 | 137 | 3 | 0 | 0 |
| IGHV4-30-2 | 119 | 130 | 2 | 71 | 1 |
| IGHV4-28 | 118 | 129 | 2 | 0 | 0 |
| IGHV4-39 | 119 | 125 | 2 | 0 | 0 |
| IGHV3-49 | 120 | 97 | 2 | 0 | 0 |
| IGHV4-4 | 118 | 96 | 2 | 0 | 0 |
| IGHV4-38-2 | 118 | 81 | 1 | 0 | 0 |
| IGHV4-61 | 119 | 81 | 1 | 0 | 0 |
| IGHV2-26 | 120 | 67 | 1 | 0 | 0 |
| IGHV2-5 | 120 | 45 | 1 | 0 | 0 |
| IGHJ3 | 36 | 0 | 0 | 0 | 0 |
| IGHJ1 | 37 | 0 | 0 | 0 | 0 |
| IGHJ5 | 36 | 0 | 0 | 0 | 0 |
| IGHJ2 | 37 | 0 | 0 | 0 | 0 |
| IGHJ6 | 40 | 0 | 0 | 0 | 0 |
IGHV * IGHJ
...YCA-RGV
QRPPEPF...Best overlap (3, 4) with score 5 which results in the following sequence:
...YCAQRXXEPF...
266 (2.56% of all input reads) reads where matched to this segment of these 62 (23.31% of all matched reads) were matched uniquely.
Cumulative value of all children (excluding unique)
Cumulative value for unique matches
| Identifier | Length | Score | Matches | Unique Score | Unique Matches |
|---|---|---|---|---|---|
| IGHV5-51 | 118 | 1.64E+04 | 188 | 2620 | 38 |
| IGHV5-10-1 | 118 | 1.308E+04 | 146 | 0 | 0 |
| IGHV1-69 | 118 | 8863 | 93 | 169 | 2 |
| IGHV1-2 | 118 | 8641 | 93 | 156 | 3 |
| IGHV1-3 | 118 | 8503 | 90 | 0 | 0 |
| IGHV1-46 | 118 | 8503 | 90 | 0 | 0 |
| IGHV1-18 | 118 | 8392 | 89 | 0 | 0 |
| IGHV1-8 | 118 | 8356 | 89 | 45 | 1 |
| IGHV1-24 | 118 | 8302 | 88 | 0 | 0 |
| IGHV1-69-2 | 118 | 6175 | 65 | 0 | 0 |
| IGHV7-4-1 | 118 | 1231 | 16 | 0 | 0 |
| IGHV3-21 | 118 | 1150 | 18 | 0 | 0 |
| IGHV3-15 | 120 | 1093 | 17 | 0 | 0 |
| IGHV3-73 | 120 | 992 | 18 | 390 | 8 |
| IGHV3-11 | 118 | 861 | 14 | 81 | 1 |
| IGHV2-70 | 120 | 571 | 9 | 131 | 2 |
| IGHV3-72 | 120 | 479 | 9 | 0 | 0 |
| IGHV3-74 | 118 | 477 | 8 | 0 | 0 |
| IGHV3-NL1 | 118 | 465 | 8 | 0 | 0 |
| IGHV3-64 | 118 | 386 | 7 | 0 | 0 |
| IGHV3-66 | 117 | 380 | 7 | 0 | 0 |
| IGHV3-48 | 118 | 380 | 7 | 0 | 0 |
| IGHV3-7 | 118 | 380 | 7 | 0 | 0 |
| IGHV3-23 | 118 | 380 | 7 | 0 | 0 |
| IGHV3-13 | 117 | 380 | 7 | 0 | 0 |
| IGHV4-34 | 117 | 376 | 5 | 151 | 2 |
| IGHV3-20 | 118 | 368 | 7 | 0 | 0 |
| IGHV1-45 | 118 | 337 | 4 | 0 | 0 |
| IGHV3-30-5 | 118 | 335 | 6 | 0 | 0 |
| IGHV3-33 | 118 | 322 | 6 | 61 | 1 |
| IGHV4-31 | 119 | 308 | 5 | 0 | 0 |
| IGHV3-53 | 117 | 306 | 6 | 0 | 0 |
| IGHV6-1 | 121 | 264 | 4 | 174 | 3 |
| IGHV3-30 | 118 | 250 | 5 | 0 | 0 |
| IGHV3-43 | 119 | 228 | 5 | 0 | 0 |
| IGHV4-59 | 117 | 206 | 3 | 0 | 0 |
| IGHV4-30-4 | 119 | 206 | 3 | 0 | 0 |
| IGHV3-49 | 120 | 183 | 4 | 0 | 0 |
| IGHV3-9 | 119 | 176 | 4 | 0 | 0 |
| IGHV1-58 | 118 | 148 | 3 | 0 | 0 |
| IGHV4-30-2 | 119 | 130 | 2 | 71 | 1 |
| IGHV4-28 | 118 | 129 | 2 | 0 | 0 |
| IGHV4-39 | 119 | 125 | 2 | 0 | 0 |
| IGHV4-4 | 118 | 96 | 2 | 0 | 0 |
| IGHV4-38-2 | 118 | 81 | 1 | 0 | 0 |
| IGHV4-61 | 119 | 81 | 1 | 0 | 0 |
| IGHV2-26 | 120 | 67 | 1 | 0 | 0 |
| IGHV2-5 | 120 | 45 | 1 | 0 | 0 |
Scores per group
Max ScoreAverage ScoreUnique Max ScoreUnique Average Score
Matches per group
MatchesUnique Matches
16 (0.15% of all input reads) reads where matched to this segment of these 2 (12.50% of all matched reads) were matched uniquely.
Cumulative value of all children (excluding unique)
Cumulative value for unique matches
Scores per group
Max ScoreAverage ScoreUnique Max ScoreUnique Average Score
Matches per group
MatchesUnique Matches
472 (4.54% of all input reads) reads where matched to this segment of these 72 (15.25% of all matched reads) were matched uniquely.
Cumulative value of all children (excluding unique)
Cumulative value for unique matches
All reads matching any Template within the CDR regions are listed here. These all stem from the alignments made in the TemplateMatching step.
CDR1
46 (0.44% of all input reads) distinct reads were matched on 40 (26.49% of all templates with CDRs) distinct templates, of these 16 (34.78% of all matched reads) were matched uniquely (on a single template). The consensus sequence is shown below.
SFY
TS
LF
T
ST
.
TY
SGY
QGMW
RML
CDR2
36 (0.35% of all input reads) distinct reads were matched on 10 (6.62% of all templates with CDRs) distinct templates, of these 25 (69.44% of all matched reads) were matched uniquely (on a single template). The consensus sequence is shown below.
PGDNMS
MSP
LNYSV
NSGD
G
S
GS
GHD
RGTKL
FLYR
| Identifier | Sequence | Template |
|---|---|---|
| Combined_2163C1642_002C1527_007 | DS......KY | IGHV2-70 |
| Combined_1308 | GMLD..SDLR | IGHV5-51 |
| C1077_002 | GSYGGSGGGF | IGHV3-30-5IGHV3-30 |
| C609_020 | LTD.....KY | IGHV2-70 |
| Combined_109Combined_1365C831_011C1850_011 | MPVD..SDLR | IGHV5-51 |
| C906_019 | MSPVD.SDLR | IGHV5-51 |
| C1453_004C1007_014 | NS......KY | IGHV2-70 |
| Combined_1531 | NSN.....TD | IGHV1-2 |
| Combined_478 | NSN.....TN | IGHV1-2 |
| Combined_2749 | PMLD..SDLR | IGHV5-51 |
| C1479_008 | PPVD..SDLR | IGHV5-51 |
| C2125_010 | SGSS..SHLL | IGHV3-21 |
| Combined_2379 | SK.......Y | IGHV2-70 |
| Combined_1063Combined_804C741_006C800_005Combined_1716Combined_3705C346_014C1767_008 | SPVD..SDLR | IGHV5-51 |
| Combined_1029Combined_3730 | SPVD..SDRL | IGHV5-51 |
| Combined_1442C1849_017 | SPVN..SDLR | IGHV5-51 |
| Combined_912 | SSGS..SHLL | IGHV3-21 |
| C503_003 | SSS....STS | IGHV5-10-1 |
| C1325_003 | SSSG..SHLL | IGHV3-21IGHV3-11 |
| Combined_914 | V......... | IGHV1-58 |
| C1886_003 | W........R | IGHV3-33 |
CDR3
20 (0.19% of all input reads) distinct reads were matched on 8 (5.30% of all templates with CDRs) distinct templates, of these 2 (10.00% of all matched reads) were matched uniquely (on a single template). The consensus sequence is shown below.
QMEDR
PGRF
SELP
NGE
LEF
P
F
D
YF
W
| Identifier | Sequence | Template |
|---|---|---|
| Combined_852Combined_2868 | DF.......W | IGHJ4IGHJ5IGHJ3IGHJ2IGHJ6 |
| Combined_3270 | DG......FW | IGHJ4IGHJ5 |
| C1655_008 | EF.......W | IGHJ4IGHJ5IGHJ1IGHJ2 |
| C2099 | ERLEE.FDFW | IGHJ4IGHJ5IGHJ1IGHJ3 |
| Combined_1466 | K......... | IGHV5-51IGHV5-10-1 |
| Combined_3663 | M........Y | IGHV5-51IGHV5-10-1 |
| Combined_1485 | MREEL.FDFW | IGHJ4IGHJ5IGHJ1IGHJ3 |
| Combined_1400 | QGSNFPALYW | IGHJ4IGHJ1 |
| Combined_1363 | QGSNFPLAYW | IGHJ4 |
| Combined_1313 | QSGNFPLAYW | IGHJ4 |
| Combined_1380Combined_096C77_006C60_021C308_022 | R......... | IGHV5-51IGHV5-10-1 |
| Combined_3703 | RPPGSYFDFW | IGHJ4IGHJ5 |
| C873_007 | RPPGYFSDFW | IGHJ4IGHJ5 |
| C362_011 | SG.......V | IGHV5-51IGHV5-10-1 |
| C495_009 | TD.......D | IGHV5-51IGHV5-10-1 |
703 (6.76% of all input reads) reads where matched to this segment of these 258 (36.70% of all matched reads) were matched uniquely.
| Identifier | Length | Order | Score | Matches | Unique Score | Unique Matches |
|---|---|---|---|---|---|---|
| REC-0-1_002 | 214 | IGKV1D-16 → IGKJ2 → IGKC | 4.906E+04 | 703 | 2.138E+04 | 258 |
252 (2.42% of all input reads) reads where matched to this segment of these 26 (10.32% of all matched reads) were matched uniquely.
| Identifier | Length | Score | Matches | Unique Score | Unique Matches |
|---|---|---|---|---|---|
| IGKV1-12 | 95 | 1.354E+04 | 142 | 67 | 1 |
| IGKV1-16 | 95 | 9697 | 105 | 0 | 0 |
| IGKV1-39 | 95 | 8997 | 98 | 0 | 0 |
| IGKV1-17 | 95 | 8868 | 96 | 0 | 0 |
| IGKV1-6 | 95 | 8422 | 92 | 0 | 0 |
| IGKV1-9 | 95 | 7207 | 82 | 0 | 0 |
| IGKV1D-43 | 95 | 7043 | 80 | 0 | 0 |
| IGKV1-NL1 | 95 | 6967 | 76 | 0 | 0 |
| IGKV1D-17 | 95 | 6727 | 77 | 0 | 0 |
| IGKV1-5 | 95 | 6619 | 72 | 0 | 0 |
| IGKV1-27 | 95 | 6340 | 70 | 0 | 0 |
| IGKV1D-13 | 95 | 6209 | 70 | 0 | 0 |
| IGKV1-8 | 95 | 4851 | 53 | 0 | 0 |
| IGKV1-33 | 95 | 3507 | 37 | 67 | 1 |
| IGKV1D-8 | 95 | 2326 | 27 | 0 | 0 |
| IGKV3D-7 | 96 | 1442 | 20 | 45 | 1 |
| IGKV3-11 | 95 | 1068 | 16 | 0 | 0 |
| IGKV3D-20 | 96 | 995 | 16 | 0 | 0 |
| IGKV3D-11 | 95 | 800 | 13 | 0 | 0 |
| IGLC7 | 106 | 747 | 14 | 291 | 6 |
| IGKV2D-26 | 100 | 669 | 10 | 413 | 6 |
| IGKV3-20 | 96 | 580 | 8 | 0 | 0 |
| IGKV3-15 | 95 | 556 | 9 | 0 | 0 |
| IGKJ5 | 12 | 427 | 6 | 0 | 0 |
| IGKJ1 | 12 | 427 | 6 | 0 | 0 |
| IGKV6-21 | 95 | 419 | 7 | 55 | 1 |
| IGKV2-24 | 100 | 369 | 7 | 157 | 3 |
| IGLV8-61 | 98 | 364 | 6 | 106 | 2 |
| IGLV5-39 | 104 | 299 | 5 | 0 | 0 |
| IGKV2D-29 | 100 | 256 | 4 | 0 | 0 |
| IGLV1-47 | 98 | 239 | 5 | 0 | 0 |
| IGLV1-44 | 98 | 233 | 5 | 0 | 0 |
| IGLV5-45 | 104 | 232 | 4 | 0 | 0 |
| IGLV4-60 | 99 | 226 | 4 | 0 | 0 |
| IGLV5-37 | 104 | 207 | 4 | 0 | 0 |
| IGKV4-1 | 101 | 190 | 3 | 0 | 0 |
| IGKV2-30 | 100 | 188 | 3 | 0 | 0 |
| IGKV2D-30 | 100 | 188 | 3 | 0 | 0 |
| IGLC6 | 106 | 184 | 2 | 0 | 0 |
| IGLC3 | 104 | 184 | 2 | 0 | 0 |
| IGLC2 | 106 | 184 | 2 | 0 | 0 |
| IGLV1-36 | 98 | 178 | 4 | 0 | 0 |
| IGLV5-52 | 105 | 153 | 3 | 0 | 0 |
| IGKV2-40 | 101 | 142 | 2 | 0 | 0 |
| IGKV2-28 | 100 | 137 | 2 | 0 | 0 |
| IGLV2-23 | 99 | 116 | 2 | 0 | 0 |
| IGLV2-14 | 99 | 116 | 2 | 0 | 0 |
| IGLV4-69 | 99 | 108 | 2 | 0 | 0 |
| IGLV10-54 | 98 | 106 | 2 | 106 | 2 |
| IGLV3-16 | 96 | 105 | 2 | 60 | 1 |
| IGLV6-57 | 98 | 102 | 2 | 0 | 0 |
| IGLV1-40 | 99 | 87 | 2 | 0 | 0 |
| IGKV5-2 | 95 | 61 | 1 | 61 | 1 |
| IGLV2-18 | 99 | 55 | 1 | 0 | 0 |
| IGLV3-9 | 95 | 55 | 1 | 0 | 0 |
| IGLV2-8 | 99 | 55 | 1 | 0 | 0 |
| IGLV2-11 | 99 | 55 | 1 | 0 | 0 |
| IGLJ2 | 12 | 54 | 1 | 54 | 1 |
| IGLV3-10 | 96 | 52 | 1 | 0 | 0 |
| IGLV1-51 | 98 | 52 | 1 | 0 | 0 |
| IGLV7-43 | 98 | 52 | 1 | 0 | 0 |
| IGLV7-46 | 98 | 0 | 0 | 0 | 0 |
| IGLV3-27 | 94 | 0 | 0 | 0 | 0 |
| IGLV3-21 | 96 | 0 | 0 | 0 | 0 |
| IGLV3-22 | 94 | 0 | 0 | 0 | 0 |
| IGLV3-25 | 96 | 0 | 0 | 0 | 0 |
| IGKJ3 | 12 | 0 | 0 | 0 | 0 |
| IGKJ4 | 12 | 0 | 0 | 0 | 0 |
| IGLJ1 | 12 | 0 | 0 | 0 | 0 |
| IGLJ6 | 12 | 0 | 0 | 0 | 0 |
| IGLJ7 | 12 | 0 | 0 | 0 | 0 |
| IGLV3-19 | 96 | 0 | 0 | 0 | 0 |
| IGLV3-1 | 95 | 0 | 0 | 0 | 0 |
240 (2.31% of all input reads) reads where matched to this segment of these 24 (10.00% of all matched reads) were matched uniquely.
Cumulative value of all children (excluding unique)
Cumulative value for unique matches
| Identifier | Length | Score | Matches | Unique Score | Unique Matches |
|---|---|---|---|---|---|
| IGKV1D-16 | 95 | 1.583E+04 | 166 | 200 | 3 |
| IGKV1-12 | 95 | 1.386E+04 | 147 | 67 | 1 |
| IGKV1-16 | 95 | 1.009E+04 | 111 | 0 | 0 |
| IGKV1-39 | 95 | 9323 | 103 | 0 | 0 |
| IGKV1-17 | 95 | 9030 | 98 | 0 | 0 |
| IGKV1-6 | 95 | 8748 | 97 | 0 | 0 |
| IGKV1-9 | 95 | 7369 | 84 | 45 | 1 |
| IGKV1D-43 | 95 | 7369 | 85 | 0 | 0 |
| IGKV1-NL1 | 95 | 7293 | 81 | 0 | 0 |
| IGKV1-5 | 95 | 6908 | 76 | 88 | 1 |
| IGKV1D-17 | 95 | 6889 | 79 | 0 | 0 |
| IGKV1-27 | 95 | 6601 | 74 | 0 | 0 |
| IGKV1D-13 | 95 | 6535 | 75 | 0 | 0 |
| IGKV1-8 | 95 | 5015 | 56 | 0 | 0 |
| IGKV1-33 | 95 | 3507 | 37 | 67 | 1 |
| IGKV1D-8 | 95 | 2490 | 30 | 0 | 0 |
| IGKV3D-7 | 96 | 1703 | 24 | 45 | 1 |
| IGKV3-11 | 95 | 1329 | 20 | 0 | 0 |
| IGKV3D-20 | 96 | 1298 | 21 | 0 | 0 |
| IGKV3D-11 | 95 | 1061 | 17 | 0 | 0 |
| IGKV3-20 | 96 | 883 | 13 | 0 | 0 |
| IGKV2D-26 | 100 | 669 | 10 | 413 | 6 |
| IGKV3-15 | 95 | 556 | 9 | 0 | 0 |
| IGKV6-21 | 95 | 419 | 7 | 55 | 1 |
| IGKV2-24 | 100 | 369 | 7 | 157 | 3 |
| IGLV8-61 | 98 | 364 | 6 | 106 | 2 |
| IGKV4-1 | 101 | 354 | 6 | 0 | 0 |
| IGLV5-39 | 104 | 299 | 5 | 0 | 0 |
| IGLV2-23 | 99 | 277 | 5 | 0 | 0 |
| IGLV2-14 | 99 | 277 | 5 | 0 | 0 |
| IGKV2D-29 | 100 | 256 | 4 | 0 | 0 |
| IGLV1-47 | 98 | 239 | 5 | 0 | 0 |
| IGLV1-44 | 98 | 233 | 5 | 0 | 0 |
| IGLV5-45 | 104 | 232 | 4 | 0 | 0 |
| IGLV4-60 | 99 | 226 | 4 | 0 | 0 |
| IGLV2-11 | 99 | 216 | 4 | 0 | 0 |
| IGLV2-18 | 99 | 216 | 4 | 0 | 0 |
| IGLV5-37 | 104 | 207 | 4 | 0 | 0 |
| IGKV2-30 | 100 | 188 | 3 | 0 | 0 |
| IGKV2D-30 | 100 | 188 | 3 | 0 | 0 |
| IGLV10-54 | 98 | 181 | 3 | 106 | 2 |
| IGLV1-36 | 98 | 178 | 4 | 0 | 0 |
| IGLV5-52 | 105 | 153 | 3 | 0 | 0 |
| IGKV2-40 | 101 | 142 | 2 | 0 | 0 |
| IGKV2-28 | 100 | 137 | 2 | 0 | 0 |
| IGLV3-9 | 95 | 110 | 2 | 0 | 0 |
| IGLV4-69 | 99 | 108 | 2 | 0 | 0 |
| IGLV3-16 | 96 | 105 | 2 | 60 | 1 |
| IGLV6-57 | 98 | 102 | 2 | 0 | 0 |
| IGLV1-40 | 99 | 87 | 2 | 0 | 0 |
| IGKV5-2 | 95 | 61 | 1 | 61 | 1 |
| IGLV2-8 | 99 | 55 | 1 | 0 | 0 |
| IGLV3-22 | 94 | 55 | 1 | 0 | 0 |
| IGLV3-21 | 96 | 55 | 1 | 0 | 0 |
| IGLV3-1 | 95 | 55 | 1 | 0 | 0 |
| IGLV3-10 | 96 | 52 | 1 | 0 | 0 |
| IGLV7-43 | 98 | 52 | 1 | 0 | 0 |
| IGLV1-51 | 98 | 52 | 1 | 0 | 0 |
| IGLV3-25 | 96 | 0 | 0 | 0 | 0 |
| IGLV3-19 | 96 | 0 | 0 | 0 | 0 |
| IGLV7-46 | 98 | 0 | 0 | 0 | 0 |
| IGLV3-27 | 94 | 0 | 0 | 0 | 0 |
Scores per group
Max ScoreAverage ScoreUnique Max ScoreUnique Average Score
Matches per group
MatchesUnique Matches
31 (0.30% of all input reads) reads where matched to this segment of these 29 (93.55% of all matched reads) were matched uniquely.
Cumulative value of all children (excluding unique)
Cumulative value for unique matches
190 (1.83% of all input reads) reads where matched to this segment of these 176 (92.63% of all matched reads) were matched uniquely.
Cumulative value of all children (excluding unique)
Cumulative value for unique matches
All reads matching any Template within the CDR regions are listed here. These all stem from the alignments made in the TemplateMatching step.
CDR1
59 (0.57% of all input reads) distinct reads were matched on 32 (16.33% of all templates with CDRs) distinct templates, of these 3 (5.08% of all matched reads) were matched uniquely (on a single template). The consensus sequence is shown below.
SAWLG
WSL
QS
S
.
S
GQS
GAEMVQW
L
CDR2
51 (0.49% of all input reads) distinct reads were matched on 25 (12.76% of all templates with CDRs) distinct templates, of these 2 (3.92% of all matched reads) were matched uniquely (on a single template). The consensus sequence is shown below.
LGSA
TS
.
.
.
.
.
S
CDR3
30 (0.29% of all input reads) distinct reads were matched on 7 (3.57% of all templates with CDRs) distinct templates, of these 27 (90.00% of all matched reads) were matched uniquely (on a single template). The consensus sequence is shown below.
QT
Y
N
L
Y
PF
Scores per group
Max ScoreAverage ScoreUnique Max ScoreUnique Average Score
Matches per group
MatchesUnique Matches
3099 (29.78% of all input reads) reads where matched to this segment of these 2971 (95.87% of all matched reads) were matched uniquely.
Scores per group
Max ScoreAverage ScoreUnique Max ScoreUnique Average Score
Matches per group
MatchesUnique Matches
3101 (29.80% of all input reads) reads where matched to this segment of these 2975 (95.94% of all matched reads) were matched uniquely.
Cumulative value of all children (excluding unique)
Cumulative value for unique matches
Length distribution
/storage/khangl/MS_benchmarking/stitch-v1.5.0-linux/batchfiles/Umab_mc.txt
-Run Info---------------
Version : 1.5
- Here the input can be defined, this will be used in the TemplateMatching and Recombine steps
Input ->
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3598.mztab
Name : EH3598
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3599.mztab
Name : EH3599
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3600.mztab
Name : EH3600
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3601.mztab
Name : EH3601
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3602.mztab
Name : EH3602
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3603.mztab
Name : EH3603
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3605.mztab
Name : EH3605
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3606.mztab
Name : EH3606
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3608.mztab
Name : EH3608
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3931.mztab
Name : EH3931
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3932.mztab
Name : EH3932
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3933.mztab
Name : EH3933
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3934.mztab
Name : EH3934
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3935.mztab
Name : EH3935
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3936.mztab
Name : EH3936
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3937.mztab
Name : EH3937
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3938.mztab
Name : EH3938
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3939.mztab
Name : EH3939
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3940.mztab
Name : EH3940
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3941.mztab
Name : EH3941
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3942.mztab
Name : EH3942
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4275.mztab
Name : EH4275
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4276.mztab
Name : EH4276
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4277.mztab
Name : EH4277
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4278.mztab
Name : EH4278
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4279.mztab
Name : EH4279
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4280.mztab
Name : EH4280
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4281.mztab
Name : EH4281
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4282.mztab
Name : EH4282
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4283.mztab
Name : EH4283
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4284.mztab
Name : EH4284
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4285.mztab
Name : EH4285
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4286.mztab
Name : EH4286
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4624.mztab
Name : EH4624
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4625.mztab
Name : EH4625
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4626.mztab
Name : EH4626
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4628.mztab
Name : EH4628
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4629.mztab
Name : EH4629
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4631.mztab
Name : EH4631
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4632.mztab
Name : EH4632
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4633.mztab
Name : EH4633
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4634.mztab
Name : EH4634
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4635.mztab
Name : EH4635
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5040.mztab
Name : EH5040
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5041.mztab
Name : EH5041
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5042.mztab
Name : EH5042
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5043.mztab
Name : EH5043
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5044.mztab
Name : EH5044
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5045.mztab
Name : EH5045
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5046.mztab
Name : EH5046
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5047.mztab
Name : EH5047
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5048.mztab
Name : EH5048
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5049.mztab
Name : EH5049
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5050.mztab
Name : EH5050
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5051.mztab
Name : EH5051
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5378.mztab
Name : EH5378
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5379.mztab
Name : EH5379
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5380.mztab
Name : EH5380
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5381.mztab
Name : EH5381
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5382.mztab
Name : EH5382
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5383.mztab
Name : EH5383
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5384.mztab
Name : EH5384
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5385.mztab
Name : EH5385
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5386.mztab
Name : EH5386
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5387.mztab
Name : EH5387
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5388.mztab
Name : EH5388
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5389.mztab
Name : EH5389
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5739.mztab
Name : EH5739
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5740.mztab
Name : EH5740
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5741.mztab
Name : EH5741
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5742.mztab
Name : EH5742
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5743.mztab
Name : EH5743
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5744.mztab
Name : EH5744
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5745.mztab
Name : EH5745
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5746.mztab
Name : EH5746
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5747.mztab
Name : EH5747
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5748.mztab
Name : EH5748
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5749.mztab
Name : EH5749
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5750.mztab
Name : EH5750
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6097.mztab
Name : EH6097
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6098.mztab
Name : EH6098
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6099.mztab
Name : EH6099
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6100.mztab
Name : EH6100
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6101.mztab
Name : EH6101
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6102.mztab
Name : EH6102
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6103.mztab
Name : EH6103
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6104.mztab
Name : EH6104
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6105.mztab
Name : EH6105
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6106.mztab
Name : EH6106
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6107.mztab
Name : EH6107
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6108.mztab
Name : EH6108
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6628.mztab
Name : EH6628
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6629.mztab
Name : EH6629
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6630.mztab
Name : EH6630
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6631.mztab
Name : EH6631
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6632.mztab
Name : EH6632
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6633.mztab
Name : EH6633
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6634.mztab
Name : EH6634
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6635.mztab
Name : EH6635
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6636.mztab
Name : EH6636
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6637.mztab
Name : EH6637
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6638.mztab
Name : EH6638
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6639.mztab
Name : EH6639
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8118.mztab
Name : EH8118
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8119.mztab
Name : EH8119
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8120.mztab
Name : EH8120
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8121.mztab
Name : EH8121
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8122.mztab
Name : EH8122
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8123.mztab
Name : EH8123
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8124.mztab
Name : EH8124
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8125.mztab
Name : EH8125
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8126.mztab
Name : EH8126
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8127.mztab
Name : EH8127
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8128.mztab
Name : EH8128
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8129.mztab
Name : EH8129
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7348.mztab
Name : EH7348
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7349.mztab
Name : EH7349
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7350.mztab
Name : EH7350
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7351.mztab
Name : EH7351
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7352.mztab
Name : EH7352
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7353.mztab
Name : EH7353
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7354.mztab
Name : EH7354
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7355.mztab
Name : EH7355
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7356.mztab
Name : EH7356
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7357.mztab
Name : EH7357
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7358.mztab
Name : EH7358
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7359.mztab
Name : EH7359
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7693.mztab
Name : EH7693
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7694.mztab
Name : EH7694
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7695.mztab
Name : EH7695
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7696.mztab
Name : EH7696
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7697.mztab
Name : EH7697
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7698.mztab
Name : EH7698
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7699.mztab
Name : EH7699
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7700.mztab
Name : EH7700
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7701.mztab
Name : EH7701
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7702.mztab
Name : EH7702
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7703.mztab
Name : EH7703
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7704.mztab
Name : EH7704
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8461.mztab
Name : EH8461
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8462.mztab
Name : EH8462
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8463.mztab
Name : EH8463
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8464.mztab
Name : EH8464
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8465.mztab
Name : EH8465
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8466.mztab
Name : EH8466
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8467.mztab
Name : EH8467
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8468.mztab
Name : EH8468
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8469.mztab
Name : EH8469
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8470.mztab
Name : EH8470
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8471.mztab
Name : EH8471
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8472.mztab
Name : EH8472
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9298.mztab
Name : EH9298
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9299.mztab
Name : EH9299
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9300.mztab
Name : EH9300
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9301.mztab
Name : EH9301
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9302.mztab
Name : EH9302
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9303.mztab
Name : EH9303
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9304.mztab
Name : EH9304
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9305.mztab
Name : EH9305
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9306.mztab
Name : EH9306
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9307.mztab
Name : EH9307
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9308.mztab
Name : EH9308
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9309.mztab
Name : EH9309
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9676.mztab
Name : EH9676
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9677.mztab
Name : EH9677
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9678.mztab
Name : EH9678
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9679.mztab
Name : EH9679
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9680.mztab
Name : EH9680
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9681.mztab
Name : EH9681
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9682.mztab
Name : EH9682
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9683.mztab
Name : EH9683
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9684.mztab
Name : EH9684
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9685.mztab
Name : EH9685
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9686.mztab
Name : EH9686
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9687.mztab
Name : EH9687
CutoffScore: 0.8
-FilterPPM : 100
<-
<-
- Template matching matches the reads defined in 'Input' to the given Templates defined in the different groups in the 'Segments'
TemplateMatching ->
EnforceUnique : 0.9
CutoffScore : 15
AmbiguityThreshold : 0.9
include!(/storage/khangl/MS_benchmarking/stitch-v1.5.0-linux/alphabets/mass_alphabet.txt)
Segments->
include!(/storage/khangl/MS_benchmarking/stitch-v1.5.0-linux/templates/Homo_sapiens_Heavy_Chain.txt)
include!(/storage/khangl/MS_benchmarking/stitch-v1.5.0-linux/templates/Homo_sapiens_Light_Chain.txt)
include!(/storage/khangl/MS_benchmarking/stitch-v1.5.0-linux/templates/common_contaminants.txt)
<-
<-
Recombine->
-Pick the highest scoring templates from each segment
N : 1
Decoy : True
CutoffScore : 10
-Separated by whitespace means directly attached
-Separated by * means with a gap attached
Order->
Homo sapiens Heavy Chain: IGHV * IGHJ IGHC
Homo sapiens Light Chain: IGLV IGLJ IGLC
<-
<-
Report ->
Folder: /storage/khangl/MS_benchmarking/stitch-v1.5.0-linux/results/{datetime} {name}/
HTML ->
Path: report-monoclonal_Umab.html
<-
FASTA ->
Path: report-monoclonal-tm_Umab.fasta
OutputType: TemplateMatching
<-
CSV ->
Path: report-monoclonal-tm_Umab.csv
OutputType: TemplateMatching
<-
FASTA ->
Path: report-monoclonal-rec_Umab.fasta
OutputType: Recombine
<-
CSV ->
Path: report-monoclonal-rec_Umab.csv
OutputType: Recombine
<-
<-
/storage/khangl/MS_benchmarking/stitch-v1.5.0-linux/alphabets/mass_alphabet.txt
Alphabet ->
Characters : ARNDCQEGHILKMFPSTWYVBZXJ.*
Identity : 8
Mismatch : -1
GapStart : -12
GapExtend : -1
PatchLength: 3
Swap : 2
Symmetric sets ->
Score: 8
Sets :>
I,L,J
<:
<-
Symmetric sets ->
Score: 6
Sets :>
N,GG
Q,AG
AV,GL,GI,GJ
AN,QG,AGG
LS,IS,JS,TV
AM,CV
NV,AAA,GGV
NT,QS,AGS,GGT
LN,IN,JN,QV,AGV,GGL,GGI,GGJ
DL,DI,DJ,EV
QT,AAS,AGT
AY,FS
LQ,IQ,AAV,AGL,AGI,AGJ
NQ,ANG,QGG
KN,GGK
EN,DQ,ADG,EGG
DK,AAT,GSV
MN,AAC,GGM
AS,GT
AAL,AAI,AAJ,GVV
QQ,AAN,AQG
EQ,AAD,AEG
EK,ASV,GLS,GIS,GJS,GTV
MQ,AGM,CGV
AAQ,NGV
<:
<-
Asymmetric sets ->
Score: 1
Sets :>
X->A,R,N,D,C,Q,E,G,H,I,L,J,K,M,F,P,S,T,W,Y,V,B,Z -Remove mismatch penalty on single gaps
A,R,N,D,C,Q,E,G,H,I,L,J,K,M,F,P,S,T,W,Y,V,B,Z->X -Remove mismatch penalty on single gaps
<:
<-
Asymmetric sets ->
Score: -4
Sets :>
.->A,R,N,D,C,Q,E,G,H,I,L,J,K,M,F,P,S,T,W,Y,V,B,Z -Add additional penalty on bigger gaps
A,R,N,D,C,Q,E,G,H,I,L,J,K,M,F,P,S,T,W,Y,V,B,Z->. -Add additional penalty on bigger gaps
<:
<-
Asymmetric sets ->
Score: 3
Sets :>
- Template sequence -- results -> in read sequence - Type
Q->E -Deamidation
N,GG->D -Deamidation
T->D -Methylation
S->T -Methylation
D->E -Methylation
R->AV,GL,GI,GJ -Methylation
Q->AA -Methylation
W->DS,AM,CV,TT -Oxidation
M->F -Oxidation
S->E -Acetylation
K->AV,GL,GI,GJ -Acetylation/Homoarginine
<:
<-
<-
/storage/khangl/MS_benchmarking/stitch-v1.5.0-linux/templates/Homo_sapiens_Heavy_Chain.txt
Homo sapiens Heavy Chain->
Segment->
Path : Homo_sapiens_IGHV.fasta
Name : IGHV
Identifier: ^(([a-zA-Z]+\d*)[\w-]*)
<-
Segment->
Path : Homo_sapiens_IGHJ.fasta
Name : IGHJ
Identifier: ^(([a-zA-Z]+\d*)[\w-]*)
<-
Segment->
Path : Homo_sapiens_IGHC.fasta
Name : IGHC
Identifier: ^(([a-zA-Z]+\d*)[\w-]*)
<-
<-
/storage/khangl/MS_benchmarking/stitch-v1.5.0-linux/templates/Homo_sapiens_Light_Chain.txt
Homo sapiens Light Chain->
Segment->
Path : Homo_sapiens_IGKV,IGLV.fasta
Name : IGLV
Identifier: ^(([a-zA-Z]+\d*)[\w-]*)
<-
Segment->
Path : Homo_sapiens_IGKJ,IGLJ.fasta
Name : IGLJ
Identifier: ^(([a-zA-Z]+\d*)[\w-]*)
<-
Segment->
Path : Homo_sapiens_IGKC,IGLC.fasta
Name : IGLC
Identifier: ^(([a-zA-Z]+\d*)[\w-]*)
<-
<-
/storage/khangl/MS_benchmarking/stitch-v1.5.0-linux/templates/common_contaminants.txt
Decoy ->
Segment ->
Path: common_contaminants.fasta
Name: Decoy
Identifier: ^sp\|[\w]*\|([\w]+)_
<-
<-
Answers to common questions can be found here. If anything is unclear, or you miss any features please reach out to the authors, all information can be found on the repository.
If the graphs are needed in a vector graphics format the whole page can be printed to a pdf. To do this print the page to a pdf file and save the generated file. These files can be imported in most vector graphics editors. It is best to turn on the background graphics and turn off any headers, besides this setting the margins smaller and using landscape or portrait could enhance the results. See the below picture for the options. If you want to be able to edit the text as text in Adobe Illustrator we had the best results using Firefox > Print > Save as PDF.
Or click here to print
The Roepstorff, Fohlman, Johnson ion nomenclature is used. This is the common way of naming ions most people will be familiar with. But we use two special ions, w and d also called satellite ions, which are not commonly used. These form by cleavages of the side chain and are thus specially suited for the disambiguation of Leucine and Isoleucine. In the overview below the mass differences and ions formed are displayed. The d ion is formed by fragmentation of the side chain of an a ion. The w ion is formed by side chain fragmentation of a z ion. Because isoleucine and threonine are doubly substituted at the beta carbon these two amino acids form two different w/d ions. THese ions are not formed with all fragmentation techniques though, Stitch only searches for d ions in the first amino acids with CID/HCD/PQD data, and only searches for w ions in ETD/ECD/EThcD/ETciD data.
Find more information here.